Question: Algorithms for identification of insertion sites using split reads
0
gravatar for xieshaojun0621
2.3 years ago by
United States
xieshaojun0621110 wrote:

Imaging I have a big insertion in the genome. Then if I sequence the sample and align the reads to the reference genome, I will get some split reads. I showed one example here. Image and video hosting by TinyPic

My plan is to identify the insertion site using these split reads.

Could anyone give me some suggestions of how to do this?

ADD COMMENTlink modified 8 weeks ago by Vitis2.1k • written 2.3 years ago by xieshaojun0621110
1
gravatar for harold.smith.tarheel
2.3 years ago by
United States
harold.smith.tarheel4.3k wrote:

We've had reasonably good success using LUMPY, which takes advantage of split reads.

ADD COMMENTlink written 2.3 years ago by harold.smith.tarheel4.3k

Thanks. I'll try it.

ADD REPLYlink written 2.3 years ago by xieshaojun0621110
0
gravatar for Vitis
8 weeks ago by
Vitis2.1k
New York
Vitis2.1k wrote:

A lot of approaches to tackle this problem. A very good discussion here:

C: Identification of the sequence insertion site in the genome

ADD COMMENTlink written 8 weeks ago by Vitis2.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1572 users visited in the last hour